PDBBioAssemblyParser (biojava 5.2.0 API)

java.lang.Object
- org.biojava.nbio.structure.io.PDBBioAssemblyParser

```
public class PDBBioAssemblyParser
extends Object
```
Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit

Author:

Peter Rose, Andreas Prlic

Constructor Summary

Constructors
Constructor Description

PDBBioAssemblyParser()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Map<Integer,BioAssemblyInfo>`	`getTransformationMap()`	Returns a map of bioassembly transformations
`void`	`pdb_REMARK_350_Handler(String line)`	Parses REMARK 350 line.
`void`	`setMacromolecularSizes()`	Set the macromolecularSize fields of the parsed bioassemblies.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - PDBBioAssemblyParser
```
public PDBBioAssemblyParser()
```
- Method Detail
  - pdb_REMARK_350_Handler
```
public void pdb_REMARK_350_Handler(String line)
```
    Parses REMARK 350 line. See format description: http://www.wwpdb.org/documentation/format33/remarks2.html
    
    Parameters:
    
    line -
  - getTransformationMap
```
public Map<Integer,BioAssemblyInfo> getTransformationMap()
```
    Returns a map of bioassembly transformations
    
    Returns:
  - setMacromolecularSizes
```
public void setMacromolecularSizes()
```
    Set the macromolecularSize fields of the parsed bioassemblies. This can only be called after the full PDB file has been read so that all the info for all bioassemblies has been gathered. Note that an explicit method to set the field is necessary here because in PDB files the transformations contain only the author chain ids, corresponding to polymeric chains, whilst in mmCIF files the transformations contain all asym ids of both polymers and non-polymers.